Blog from March, 2016

March Monthly Meeting

The March Monthly Meeting was so packed that we had a CDI Forum post about it.

We had two presentations:

CyberGIS and CEGIS

Johnathan Rush and Mike Finn

A great example of a USGS-academia collaboration, making open GIS tools.

I 

Anyone can create an account - check out the TopoLens and other apps.
They welcome feedback and suggestions!

Digital Grain Size App

 Daniel Buscombe

A FY15 CDI-funded project allowing users to get grain size distributions for sediment-related research quickly and easily.



 

Virtual Training Topics

We also opened voting for the Virtual Training Topics for this year.

Options are: Reviewing Metadata & Using Controlled Vocabularies; Git, GitHub, & Stash; Scientific workflow and reproducibility; ScienceBase R Package: sbtools; and VisTrails Workflow Software. Vote before April 13, 2016.

In mid-April we will take stock of the results and plan to incorporate them into this year’s CDI Virtual Annual Meeting.

Vote now!


At the last Tech Stack Working Group meeting, Felipe Fernandes (http://ocefpaf.github.io/) discussed some of the new python packages such as mplleaflet and folium, which are making it possible to create dynamic maps using leaflet in the browser without writing any JavaScript code.

Some useful links:


The next TSWG meeting is 4/21/16 on The New Geoplatform.Gov
Geoplatform.gov was recently rebuilt from the ground up. Jerry will talk about new features of the platform and plans for the future.


Check out the Tech Stack WG Meetings page for more info.

Time for a webinar round-up. There were a number of useful "external" (non-CDI) webinars over the past two weeks. (Sometimes it seems like my eyes are glued to WebEx for a very large proportion of the day.) If you didn’t get a chance to watch these, here is a quick run-down and some links. 

DataONE Webinar. Research Computing Skills for Scientists: Lessons, Challenges, and Opportunities from Software Carpentry

Greg Wilson, Software Carpentry

3/8/16: Greg’s account of lessons learned from years of Software Carpentry workshops contained some really interesting and useful nuggets for anyone who wants to teach anything effectively. Team teaching for feedback and improvement, iteration on lesson plans by a large group of instructors and students, and advertising specific tools (python, github) as opposed to abstract concepts (automation of tasks, version control) are some of the points he discussed. He suggested checking out the book How Learning Works: Seven Research-Based Principles for Smart Teaching by Ambrose et al. That book is now sitting on my shelf as a result of interlibrary loan, and I hope to look at it before it is overdue.

Video, slides, and discussion

EarthCube Webinar Series: Doing Science with EarthCube Tools. Cyber Tools for Research: A Tour through the Hardware Store of Useful Tools for Managing your Data and Research Work

Ouida Meier, EarthCube CRESCYNT - Coral Reef Science and Cyberinfrastructure Network, University of Hawaii

3/11/16: Ouida gave a tour of a long list of tools for research. Some of the categories of tools she reviewed are: collaboration, workflows, repositories, statistical data analysis, data visualization, mapping, protocols, unique identifiers, metadata creation, image management, audio manipulation and analysis, biological taxonomy, and learning to code. The video is available now at the YouTube link, and I suggest skimming through the slides once they are posted on the webinar series page. There are several tools that I’d not heard of, and I want to check out.

YouTube video

Slides to be posted on the Webinar Series Page


USGS Core Science Systems Brown Bag: A Map for the Future: The Protected Areas Database of the US (PAD-US)

Lisa Johnson, USGS Gap Analysis Program (GAP) / PAD-US Coordinator

3/16/16: What can you do with a Protected Areas Database? At first I had no idea, but Lisa ran through several applications such as analyzing how much of a species habitat is protected, searching for park lands with specific features, and getting more accurate maps of protected areas than shown in Google Maps! PAD-US is the nation’s inventory of protected public areas, it connects disparate efforts and reduces duplication among the many organizations that deal with these areas. Visit PAD-US at gapanalysis.usgs.gov/padus. The project team welcomes new applications for their data and new potential partners.

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Recent USGS Community for Data Integration Blog posts


The data management group met on 3/14 with two main topics: a report out on the recent USGS Public Access Plan “Implementation Meeting”, and a presentation on the Southeast Region Data Managers group.

Slides and recordings are at the Data Management Wiki space for DMWG Meeting 2016_03_14.

USGS Public Access Plan Implementation Meeting (Viv Hutchison)

This meeting was held in Reston, VA, March 1-3, 2016, its purpose was to develop a roadmap for moving forward to meet the USGS Public Access Plan. Attendees, who represented many areas of USGS including OSQI, CSASL, OEI, SPN, WRET, and more, reviewed current processes/workflows/systems involved for publications and data release, then identified needs and gaps to achieving success.

Breakout groups were formed for

  • USGS systems connections & workflows (Jim Kreft, CIDA)

  • Training and Communications (Keith Kirk, OSQI)

  • Repositories and Storage (Keith Richmond, OEI)

You can join these sub-teams! Contact the leads or Viv Hutchison.

You can also get information about monthly meetings of the entire group (TBD) by filling out this form.

(See pptx)

Southeast Region Data Management Working Group (Cassandra Ladino)

The Southeast Region Data Management Workgroup was created by the Region Director to help Science Centers are up to speed before the October 1, 2016 date for implementing the recent data policy memos. One or two representatives from each center have joined to lead a community of practice and facilitate access to tools and expertise needed to implement data lifecycle management.

Their current activities include development of:

  • Operations Strategy template (describing common technical solutions, operating procedures, and rules)

  • Data Management Plan template (for scientists to satisfy proposal requirements)

The group welcomes more diverse input in their conversations and invites you to join. (See PDF) Contact ccladino@usgs.gov.

The Semantic Web Working Group met on March 10th and learned about the NERC Vocabulary Services at the British Oceanographic Data Centre.
Rob Thomas and Alexandra Kokkinaki gave an overview and demo of the vocabulary services, which use SKOS concepts, collections, and schemes.

They demoed:

A “human friendly” search for vocabularies and terms within vocabularies:
https://www.bodc.ac.uk/data/codes_and_formats/vocabulary_search/

A SPARQL endpoint for the vocabulary services:
http://vocab.nerc.ac.uk/sparql/

The NERC Vocabulary Server has been used operationally for more than ten years!


https://www.bodc.ac.uk/data/codes_and_formats/vocabulary_search/

Scientist's Challenge

I'm really excited about a new series that we kicked off yesterday during the CDI March Monthly Meeting

The Scientist's Challenge is an opportunity for CDI to hear from members or other USGS researchers about an issue they are trying to solve.

 Scientist's Challenge

On the CDI Forum, there's a post about How it Works, and a post about Rich McDonald's presentation yesterday.

Rich presented questions his group has about building an API to connect USGS remotely sensed data and a desktop application on surface water flow and sediment transport.

Anyone with ideas or feedback can post on the forum. Luckily, there was a post even before the end of the Monthly Meeting! I continue to be very impressed with CDI's breadth of expertise.

If you or someone you know has a challenge that would fit this series, please get in touch with us at cdi@usgs.gov.

The Connected Devices Working Group (CDWG) hosted a presentation and discussion about ScienceCache on 2/25 by Megan Eberhardt-Frank and Thom Miller. ScienceCache, a CDI funded project from FY15, targets geo-cachers and youth for citizen science data collection. Projects can be built by scientists that specify locations or goals for new data collection sites, including clues, questions, measurements, and other activities.

Current projects using ScienceCache include huckleberry phenology data and tree invasion repeat photography, but investigators can create routes for their own types of data collection.

ScienceCache code will be made available at the USGS Stash Repository.

The CDI Connected Devices Working Group meets the fourth Thursday of the month at noon ET (11am CT/10am MT/9am PT/8am Anchorage/6am Hawaii). See the CDWG Meetings Wiki page for recent meetings.